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Dear Marilyn The 1998 article by Brenner et al discusses your question 1. Brenner SE, Chothia C, Hubbard TJ. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc Natl Acad Sci U S A. 1998 May 26;95(11):6073-8. http://www.pnas.org/cgi/content/full/95/11/6073 As fig 3 shows, the length of the alignment is crucial http://www.pnas.org/cgi/content/full/95/11/6073/F3 Regards Daniel On Wed, 2005-09-21 at 16:43 -0500, Yoder, Marilyn wrote: > My 'googling' skills are failing me and thought perhaps someone here > could point me in the right direction. > > I have two questions. > > 1. It is often stated that with ~30% sequence identity, protein folds > will likely be similar. I can't find a reference to this > 'rule-of-thumb'. I suspect there has been a systematic study showing > this to be the case, but I can't put my finger on it. > > 2. I'm looking for examples where proteins of some size, at least 100 > amino acids, have sequence identity of ~30% but do not have similar > folds. Again, I'm having difficulties finding such and would > appreciate any examples anyone can provide. (Wasn't there a contest > or something where investigators were challenged to introduce the > minimal sequence change that generated a 'different' structure?). > > Many thanks, > Marilyn Yoder > > Marilyn D. Yoder > Division of Cell Biology and Biophysics > University of Missouri-Kansas City > 5007 Rockhill Rd. > Kansas City, MO 64110-2499 > phone: 816-235-1986 > fax: 816-235-1503 > -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K.
